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PhD Studentships: Reef Structural Complexity and the Dwindling Habitat for Diverse Caribbean Fish Communities

Charlie Dryden

Newcastle University

Supervisor(s): Nick Polunin & Steve Newman

Scleractinian corals are ‘ecosystem engineers’, providing most of the foundations of the coral reef ecosystem, specifically creating a three-dimensional physical habitat and micro-climatic conditions for a plethora of species and ecosystem services. Corals act as a refuge from predators, provide habitat surfaces for prey and offer nesting sites for brooding species. Threats to the existence of coral reefs such as climate-related bleaching, diseases, nutrient susceptibility and fishing-related impacts, have created an urgent need to more fully understand the role corals, and the habitat they create, play in supporting the diverse and abundant coral reef communities.

Early work on coral reef degradation focussed largely on phase shifts from coral to algal dominated states and effects on community structure. This rather ignored the role of the physical structure of the reef sustained by corals. Structural complexity has been correlated with higher levels of diversity in both terrestrial and marine habitats, including coral reefs. However, these findings relied upon simplistic habitat measures and broad community metrics. It is necessary for this relationship to be examined in greater detail to identify which aspects of structural complexity are important to specific components of the community. Related to this, there is scarcely anything known about how mobile species interact with the reef framework. Yet the utilisation of space on reefs by fish is key to predicting how degradation will affect the ecosystem and the humans that rely on them. Such understanding will offer insight into how species, trophic groups and size classes react to loss of habitat structure.

The Caribbean has been undergoing continued losses of structurally complex Acropora spp. and Montastraea spp. of coral since the late 1970s. Stress-tolerant corals that form smaller and less complex colonies, such as Porites spp. and Agaricia spp. have now become relatively more abundant and the consequences of this shift are scarcely known. While the coral cover of Caribbean reefs has been declining for 40 years, changes in fish community structure were negligible until 10 years ago. These changes in the Caribbean fish communities are thus unlikely to be exclusively linked to live coral-cover loss. Unlike their Indo-Pacific counterparts, no Caribbean reef fish are obligately dependent on living corals for food or refuge, therefore decline in reef fish communities appears to more closely relate to generic effects of the loss of reef structure.

Temporal trends in Caribbean reef complexity and community structure have been explored through sparse existing data however, there is at present no methodologically-constrained information on spatial trends in Caribbean regional complexity, yet this is crucial for understanding the current status of reefs, the extent of ongoing changes, and the implications for environmental managers.

This study will examine the concept of structural complexity in natural systems and detail the spatial patterns of reef complexity across 10 Caribbean countries. It will then focus on the relationship between complexity and the fish community and the behavioural interactions between fish and the reef structure.

Marine Science and Technology
Newcastle University NE1 7RU


PhD Studentships: Sensory Ecology, Parasites and Mate Choice in the Guppy, POECILIA RETICULATA

Jessica Stephenson

Cardiff University & Bristol University

Supervisor(s): Joanna Cable & Gabrielle Archard, & Julian Partridge

My research focuses on the way information from different sensory systems (vision and olfaction) interact to inform animal decisions. I am using the guppy-gyrodactylid model system to test how parasitism affects this interaction in a mate choice context. In dissecting the mechanism by which parasitism can alter mate choice in this host, the project will increase understanding of how sexual selection changes in parasitized populations. Furthermore, this could provide an explanation for the maintenance of anomalously high Major Histocompatibility Complex (MHC) allelic diversity in parasitized fish populations.

How an individual’s mate choice preferences change over time is an understudied area of evolutionary ecology. Condition-dependent variation in mate choice preferences between individual female guppies has been demonstrated. It is likely, though little tested, that there is also within-individual variation in preference because condition will change through time. One mechanism by which preferences may vary both between and within individuals is through alteration in the rank females attribute to each of the several cues used during mate choice. These cues in guppies have been well studied; in healthy females mate choice appears to be based largely on visual cues, females prefer males with intense carotenoid colouration and high display rate. The role of olfaction in guppy mate choice has received little attention and is uncertain, though it is through olfaction that animals (including fish) assess MHC compatibility. Susceptibility to parasites is linked to MHC genotype in guppies, so choosing mates based on MHC compatibility is likely to increase guppy reproductive fitness. Olfactory cues may also serve to ‘prime’ the visual system, as has been found in zebrafish. I am using a range of behavioural experiments to test hypotheses relating to condition dependent, within individual variation in the use of information from different sensory modalities in a mate choice context.


Cardiff School of Biosciences,
Biomedical Sciences Building,
Museum Avenue,
CF10 3AX


PhD Studentship: A Genomic approach to the Genetic Impact of an Invasive Congener on a threatened native pond fish

Daniel Jeffries

University of Hull & Cefas-Lowestoft

Supervisor(s): Bernd Hänfling, Lori Lawson-Handley & Gordon Copp

Research on invasive species and invaded communities is essential to understanding and predicting biodiversity change. Furthermore, introduced species are excellent model systems with which to address fundamental questions in biology. However, biological invasions can have dramatic impacts on native species and this appears to be the case for the crucian carp Carassius carassius, which is native to northwestern Europe (including southeast England), and under threat from non-native congeners goldfish C. auratus and gibel (a.k.a. Prussian) carp C. gibelio. Conservation efforts for C. carassius are hampered by the taxonomic ambiguity which exists between C. carassius, C. auratus and C. gibelio; the problems in classifying and identifying separate Carassius spp. have introduced doubt regarding the current distributions of all Carassius spp. Consequently, impact assessment has been difficult; for example, it has only recently been demonstrated that around 70% of pure C. carassius populations in Norfolk, UK have been replaced by non-native Carassius species in the past 30 years.

In order to provide impact assessments in invasive systems, conservation geneticists have previously concentrated their studies on the lowered fitness and adaptability of native species in small populations due to the loss of genetic variability. These studies almost exclusively use near-neutral genetic markers, which cannot be a proxy for genetic variation in genes which have selectively important functions. Furthermore, neutral markers will lose genetic variation more rapidly than those under selection, with there being no correlation between molecular marker heterozygosity and heritabilities. There is likely therefore to be a difference between the impact of bottlenecks and/or climate change on genetic variation in neutral and non-neutral genes. Additionally, the study of hybridisation has been carried out previously using mainly only a small number of molecular markers, which do not have sufficient power to reveal the introgression of single genes. These limitations have left two fundamental evolutionary questions unanswered: to what extent is adaptively important genetic variation affected by bottlenecks in small, isolated populations, and, what are the genetic effects associated with environmental change (through invasive species and climate change) on fragmented populations?

With the development of next-generation sequencing, it is now feasible to address these research gaps. Next generation sequencing techniques allow for genome-wide sequencing, including selectively functional genes, thus providing a better representation of the genetic variation within individuals and populations and allowing for comparison between the behaviour of these genome regions during bottlenecks. Furthermore, these techniques allow for the identification of small regions in the genome of native species that have introgressed from non-natives or vice versa. Simultaneously, the genomic analyses of this system, in conjunction with microsatellite analyses, will shed light on the genetic structure of C. carassius populations in both the UK and continental Europe, providing the means to put forward comprehensive and much needed Biodiversity action plans for this threatened species.


Daniel Jeffries
Evolutionary Biology Group
Hardy Building
University of Hull


PhD Studentship: The Structure and Function of Social Networks in a Marine Predator

David Jacoby

Marine Biological Association & University of Exeter

Supervisor(s): Darren Croft and David Sims

It is well documented that many species of shark exhibit frequent, and often sexually segregated, aggregation behaviour during the resting phase of their diel cycle. This behaviour has been linked in the past to habitat or environmental preferences, foraging opportunities and reproductive behaviour, but little attention has been paid to the role of social preferences in these aggregations. Social network analysis is a theoretical framework which has been recently adapted to explore how animals interact through space and time, and consequently what impact this has on the transmission of information or disease between conspecifics. With elasmobranchs exhibiting a larger brain mass to body mass ratio than teleost fish, there is potential for the formation of complex social systems within these aggregation events but this has never been examined.

This project uses the small spotted catshark (Scyliorhinus canicula) as a model species with which to study social preferences and network construction in elasmobranchs. Using repeatable and controlled laboratory network experiments this project aims to determine the role of kinship and familiarity on the development of social structure in this species and assess how habitat complexity is likely to influence decisions about social behaviour. To give context to the laboratory studies, nearly 50 adult catsharks have been tagged acoustically and are currently being tracked in the wild with passive telemetry receivers on the seabed. Network analysis will not only shed light on the degree of co-occurrence of these sharks in the wild but will also be adapted to understand how environmental variables influence the ways in which individual, or groups of, animals move within and between habitat areas. The technique adapted for this study will have implications for the analysis of telemetry data from a wide variety of both marine and terrestrial animals.


Griffiths, A.M., Jacoby, D.M.P., Casane, D., McHugh, M., Croft, D.P., Genner, M.J. & Sims, D.W. First analysis of multiple paternity in an oviparous shark, the small-spotted catshark (Scyliorhinus canicula L.). Journal of Heredity (in press) doi: 10.1093/jhered/esr112

Jacoby, D.M.P., Croft, D.P. & Sims, D.W. Social behaviour in sharks and rays: analysis, patterns and implications for conservation. Fish and Fisheries (in press) doi: 10.1111/j.1467-2979.2011.00436.x

Jacoby, D.M.P., Busawon, D.S. & Sims, D.W. (2010). Sex and social networking: the role of male presence on social structure of female shark groups. Behavioral Ecology 21, 808-818.


The Marine Biological Association of the UK
The Laboratory
Citadel Hill

PhD Studentship: Validation and Development of Otolith Microchemistry in free-ranging Marine Fish

Anna Sturrock

University of Southampton

Supervisor(s): Dr Clive Trueman, Dr Ewan Hunte

The aim of the project is to determine the relationship between otolith microchemistry and the ambient environmental conditions experienced by free-swimming plaice (Pleuronectes platessa L.). By matching known spatial and temporal movements with otolith composition, we hope to validate and develop otolith microchemistry as a useful tool in marine fish spatial ecology, and will use the results to complete our understanding of the lifetime movements and stock structure of North Sea plaice.

Data records from free-ranging plaice tagged with electronic data storage tags (DSTs) will be used to provide an independent measure of location with which to compare trace element and stable isotope composition of concomitant otolith material. Also, the physical and chemical environments experienced during the plaice lifecycle will be analysed and used to construct predictive maps of otolith composition.

Otolith microchemistry provides a promising ‘natural tag’ with which to retrospectively track movements of wild fish, but it has yet to be applied widely to fully marine species. The project aims to provide in situ validation of this technique and produce predictive maps that could ultimately remove the need for extensive otolith reference collections for future studies in the North Sea. Also, the information on plaice spatial dynamics derived from this study will be considered both in terms of implications for current management strategies, and how data derived from otolith microchemistry might best be applied to marine fisheries management in the future. |

Symposium 2019: Call for Abstracts. Deadline Extended

We welcome contributions for oral or poster presentations on the topic of “Advances in eDNA-based Approaches to Fish Ecology and Management”. Please take account of the symposium sub-themes when submitting your abstract. Potential contributors should submit abstracts for oral, poster presentation or 3 minute speed-talk following the template shown below. The scientific steering committee will review all abstracts for relevance to the symposium and scientific merit before compiling the programme.

Continue reading “Symposium 2019: Call for Abstracts. Deadline Extended”